I have a 93 ranger 2.3 5 speed manual and when I'm going above 45 in 3rd 4th or 5th it vibrates really bad but only when I'm pushing on the gas pedal it also does it in neutral if I'm coasting 45 or above. It will also do it if I push on the clutch pedal. It also wines really bad especially in 5th. I'm thinking an input shaft bearing? Imnot sure though. When I had the tranny out to replace the clutch I noticed the input shaft would move about a quarter inch when I wiggled it. Any help would be awesome. Thank you in advance.

You can rule out the input shaft bearing if it vibrates while your foot is on the clutch. However, a quarter inch of endplay is a LOT. The type of vibration you are describing really sounds like a bad u-joint.

The whining in 5th gear could be because that gear is getting worn out.

Okay. Bad u joint was my next guess. I'm not sure which one is fifth but I know when I opened the tranny up I noticed the gear closest to the bellhousing of the tranny on top looked pretty worn. All the teeth were there just wore down pretty bad.

5th gear would be the biggest one on the input shaft, meshing with the smallest one on the output shaft. It's more common for 5th gear to wear out than other gears, think about it, you are in 5th gear more than the rest.